The World Cancer Research Fund and the American Institute for Cancer Research recommend a plant-based diet to cancer survivors, which may reduce chronic inflammation and excess adiposity associated with worse survival. We investigated associations of plant-based dietary patterns with inflammation biomarkers and body composition in the Pathways Study, in which 3659 women with breast cancer provided validated food frequency questionnaires approximately 2 months after diagnosis. We derived three plant-based diet indices: overall plant-based diet index (PDI), healthful plant-based diet index (hPDI) and unhealthful plant-based diet index (uPDI). We assayed circulating inflammation biomarkers related to systemic inflammation (high-sensitivity C-reactive protein [hsCRP]), pro-inflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α) and anti-inflammatory cytokines (IL-4, IL-10, IL-13). We estimated areas (cm2) of muscle and visceral and subcutaneous adipose tissue (VAT and SAT) from computed tomography scans. Using multivariable linear regression, we calculated the differences in inflammation biomarkers and body composition for each index. Per 10-point increase for each index: hsCRP was significantly lower by 6·9 % (95 % CI 1·6%, 11·8%) for PDI and 9·0 % (95 % CI 4·9%, 12·8%) for hPDI but significantly higher by 5·4 % (95 % CI 0·5%, 10·5%) for uPDI, and VAT was significantly lower by 7·8 cm2 (95 % CI 2·0 cm2, 13·6 cm2) for PDI and 8·6 cm2 (95 % CI 4·1 cm2, 13·2 cm2) for hPDI but significantly higher by 6·2 cm2 (95 % CI 1·3 cm2, 11·1 cm2) for uPDI. No significant associations were observed for other inflammation biomarkers, muscle, or SAT. A plant-based diet, especially a healthful plant-based diet, may be associated with reduced inflammation and visceral adiposity among breast cancer survivors.

A series of organoclays with monolayers, bilayers, pseudotrilayers, paraffin monolayers and paraffin bilayers were prepared from montmorillonite by ion exchange with hexadecyltrimethylammonium bromide (HDTMAB). The HDTMAB concentrations used for preparing the organoclays were 0.5, 0.7, 1.0, 1.5, 2.0 and 2.5 times the montmorillonite cation exchange capacity (CEC). The microstructural parameters, including the BET-N2 surface area, pore volume, pore size, and surfactant loading and distribution, were determined by X-ray diffraction, N2 adsorption-desorption and high-resolution thermogravimetric analysis (HRTG). The BET-N2 surface area decreased from 55 to 1 m2/g and the pore volume decreased from 0.11 to 0.01 cm3/g as surfactant loading was increased from Na-Mt to 2.5CEC-Mt. The average pore diameter increased from 6.8 to 16.3 nm as surfactant loading was increased. After modifying montmorillonite with HDTMAB, two basic organoclay models were proposed on the basis of HRTG results: (1) the surfactant mainly occupied the clay interlayer space (0.5CEC-Mt, 0.7CEC-Mt, 1.0CEC-Mt); and (2) both the clay interlayer space and external surface (1.5CEC-Mt, 2.0CEC-Mt, 2.5CEC-Mt) were modified by surfactant. In model 1, the sorption mechanism of p-nitrophenol to the organoclay at a relatively low concentration involved both surface adsorption and partitioning, whereas, in model 2 it mainly involved only partitioning. This study demonstrates that the distribution of adsorbed surfactant and the arrangement of adsorbed HDTMA+ within the clay interlayer space control the efficiency and mechanism of sorption by the organoclay rather than BET-N2 surface area, pore volume, and pore diameter.

We present an overview of the Middle Ages Galaxy Properties with Integral Field Spectroscopy (MAGPI) survey, a Large Program on the European Southern Observatory Very Large Telescope. MAGPI is designed to study the physical drivers of galaxy transformation at a lookback time of 3–4 Gyr, during which the dynamical, morphological, and chemical properties of galaxies are predicted to evolve significantly. The survey uses new medium-deep adaptive optics aided Multi-Unit Spectroscopic Explorer (MUSE) observations of fields selected from the Galaxy and Mass Assembly (GAMA) survey, providing a wealth of publicly available ancillary multi-wavelength data. With these data, MAGPI will map the kinematic and chemical properties of stars and ionised gas for a sample of 60 massive (${>}7 \times 10^{10} {\mathrm{M}}_\odot$) central galaxies at $0.25 < z <0.35$ in a representative range of environments (isolated, groups and clusters). The spatial resolution delivered by MUSE with Ground Layer Adaptive Optics ($0.6-0.8$ arcsec FWHM) will facilitate a direct comparison with Integral Field Spectroscopy surveys of the nearby Universe, such as SAMI and MaNGA, and at higher redshifts using adaptive optics, for example, SINS. In addition to the primary (central) galaxy sample, MAGPI will deliver resolved and unresolved spectra for as many as 150 satellite galaxies at $0.25 < z <0.35$, as well as hundreds of emission-line sources at $z < 6$. This paper outlines the science goals, survey design, and observing strategy of MAGPI. We also present a first look at the MAGPI data, and the theoretical framework to which MAGPI data will be compared using the current generation of cosmological hydrodynamical simulations including EAGLE, Magneticum, HORIZON-AGN, and Illustris-TNG. Our results show that cosmological hydrodynamical simulations make discrepant predictions in the spatially resolved properties of galaxies at $z\approx 0.3$. MAGPI observations will place new constraints and allow for tangible improvements in galaxy formation theory.

An increasing number of unexpectedly diverse benthic communities are being reported from microbially precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded its greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semilandmarks) to investigate morphological variance through time to better understand the ecological consequences of the end-Permian mass extinction and to examine the hypothesis that microbial mats played a key role in ostracod survival. Our results show that taxonomic diversity and morphological disparity were decoupled during the end-Permian extinction and that morphological disparity declined rapidly at the onset of the end-Permian extinction, even though the high diversity of ostracods initially survived in some places. The decoupled changes in taxonomic diversity and morphological disparity suggest that the latter is a more robust proxy for understanding the ecological impact of the extinction event, and the low morphological disparity of ostracod faunas is a consequence of sustained environmental stress or a delayed post-Permian radiation. Furthermore, the similar morphological disparity of ostracods between microbialite and non-microbialite facies indicates that microbial mats most likely represent a taphonomic window rather than a biological refuge during the end-Permian extinction interval.

Previous studies have revealed associations of meteorological factors with tuberculosis (TB) cases. However, few studies have examined their lag effects on TB cases. This study was aimed to analyse nonlinear lag effects of meteorological factors on the number of TB notifications in Hong Kong. Using a 22-year consecutive surveillance data in Hong Kong, we examined the association of monthly average temperature and relative humidity with temporal dynamics of the monthly number of TB notifications using a distributed lag nonlinear models combined with a Poisson regression. The relative risks (RRs) of TB notifications were >1.15 as monthly average temperatures were between 16.3 and 17.3 °C at lagged 13–15 months, reaching the peak risk of 1.18 (95% confidence interval (CI) 1.02–1.35) when it was 16.8 °C at lagged 14 months. The RRs of TB notifications were >1.05 as relative humidities of 60.0–63.6% at lagged 9–11 months expanded to 68.0–71.0% at lagged 12–17 months, reaching the highest risk of 1.06 (95% CI 1.01–1.11) when it was 69.0% at lagged 13 months. The nonlinear and delayed effects of average temperature and relative humidity on TB epidemic were identified, which may provide a practical reference for improving the TB warning system.

Porphyromonas gingivalis has been linked to the development and progression of oesophageal squamous cell carcinoma (ESCC), and is considered to be a high-risk factor for ESCC. Currently, the commonly used methods for P. gingivalis detection are culture or DNA extraction-based, which are either time and labour intensive especially for high-throughput applications. We aimed to establish and evaluate a rapid and sensitive direct quantitative polymerase chain reaction (qPCR) protocol for the detection of P. gingivalis without DNA extraction which is suitable for large-scale epidemiological studies. Paired gingival swab samples from 192 subjects undergoing general medical examinations were analysed using two direct and one extraction-based qPCR assays for P. gingivalis. Tris-EDTA buffer-based direct qPCR (TE-direct qPCR), lysis-based direct qPCR (lysis-direct qPCR) and DNA extraction-based qPCR (kit-qPCR) were used, respectively, in 192, 132 and 60 of these samples for quantification of P. gingivalis. The sensitivity and specificity of TE-direct qPCR was 95.24% and 100% compared with lysis-direct qPCR, which was 100% and 97.30% when compared with kit-qPCR; TE-direct qPCR had an almost perfect agreement with lysis-direct qPCR (κ = 0.954) and kit-qPCR (κ = 0.965). Moreover, the assay time used for TE-direct qPCR was 1.5 h. In conclusion, the TE-direct qPCR assay is a simple and efficient method for the quantification of oral P. gingivalis and showed high sensitivity and specificity compared with routine qPCR.

The aim of this study was to develop and externally validate a simple-to-use nomogram for predicting the survival of hospitalised human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) patients (hospitalised person living with HIV/AIDS (PLWHAs)). Hospitalised PLWHAs (n = 3724) between January 2012 and December 2014 were enrolled in the training cohort. HIV-infected inpatients (n = 1987) admitted in 2015 were included as the external-validation cohort. The least absolute shrinkage and selection operator method was used to perform data dimension reduction and select the optimal predictors. The nomogram incorporated 11 independent predictors, including occupation, antiretroviral therapy, pneumonia, tuberculosis, Talaromyces marneffei, hypertension, septicemia, anaemia, respiratory failure, hypoproteinemia and electrolyte disturbances. The Likelihood χ2 statistic of the model was 516.30 (P = 0.000). Integrated Brier Score was 0.076 and Brier scores of the nomogram at the 10-day and 20-day time points were 0.046 and 0.071, respectively. The area under the curves for receiver operating characteristic were 0.819 and 0.828, and precision-recall curves were 0.242 and 0.378 at two time points. Calibration plots and decision curve analysis in the two sets showed good performance and a high net benefit of nomogram. In conclusion, the nomogram developed in the current study has relatively high calibration and is clinically useful. It provides a convenient and useful tool for timely clinical decision-making and the risk management of hospitalised PLWHAs.

The association between opportunistic infection (OI) and anaemia among HIV-infected patients remains to be studied. We investigated the prevalence and risk factors of anaemia in hospitalised HIV-infected patients to reveal the association between OI and anaemia. We conducted a retrospective study of HIV-positive hospitalised patients from June 2016 to December 2017 in Mengchao Hepatobiliary Hospital of Fujian Medical University. Patients’ information on socio-demographic and clinical characteristics were carefully collected. The comparison of anaemia prevalence between groups was conducted with χ2 test. A logistic regression model was carried out to analyse the predictors of anaemia. The total prevalence of anaemia in hospitalised HIV-infected patients was 55.15%. The prevalence of mild, moderate and severe anaemia was 41.42%, 11.08% and 2.64%, respectively. Predictors independently associated with anaemia were: CD4 counts <50 cells/μl (odds ratio (OR): 6.376, 95% confidence interval (CI) = 1.916–21.215, P = 0.003), CD4 counts 50–199 cells/μl (OR: 6.303, 95% CI = 1.874–21.203, P = 0.003), co-infection with tuberculosis (TB) (OR: 2.703, 95% CI = 1.349–5.414, P = 0.005) or Penicillium marneffei (PM) (OR: 7.162, 95% CI = 3.147–15.299, P < 0.001). In Fujian, China, more than half inpatients with HIV were anaemic, but severe anaemia is infrequent. Lower CD4 counts, co-infection with TB or PM were independent risk factors for anaemia. Chinese HIV patients especially with TB, PM infection and low CD4 level should be routinely detected for anaemia to improve therapy.

Adult Glioblastomas (GBMs) remain one of the least curable brain cancers despite the discovery and use of DNA alkylating agent Temozolomide (TMZ). TMZ provides a moderate survival benefit to sensitive patients whose O6-methylguanine-methyltransferase (MGMT) gene is silenced by promoter methylation. Unfortunately, TMZ potential is stunted because of the rapid onset of tumour recurrence and acquired resistance believed to result from the upregulation of DNA damage repair by the base excision repair (BER), mismatch repair (MMR), or homologous recombination (HR) systems. Our laboratory previously demonstrated that cell lines obtained from recurrent, TMZ-resistant GBMs could be re-sensitized to TMZ when treated with an inhibitor of poly (ADP-ribose) polymerase-1 (PARP-1) – a protein instrumental in the recruitment of BER machinery. From this preliminary research, we postulate that PARP-1 inhibition may not only be used to overcome established resistance in GBM but may also be used to prevent its emergence altogether. To test this hypothesis, we utilized the MGMT-methylated GBM cell line U251N and developed an in vitro model of inducible TMZ resistance. We verified that prolonged treatment of U251N cells with TMZ resulted in the emergence of resistant colonies that resembled recurrent GBM clinically observed in TMZ-treated patients. However, when the parental U251N line was co-treated with TMZ and PARP-1 inhibitor ABT-888, resistant colonies failed to appear. Therefore, PARP-1 inhibition may possess the potential to maintain tumour sensitivity to TMZ as well as evade the otherwise inevitable development of resistance in GBM.

The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source emission cooled from approximately 6 400 K to 2 100 K over a 7-d period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (~2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor.

Biomimetic motions are helpful to underwater vehicles and new conception airplanes design. The lattice Boltzmann method with an immersed boundary method technique is used to reveal the propulsion and lift enhancement mechanism of biomimetic motions. The flow past a sphere and an ellipsoidal flapping wing were validated respectively by comparing with other numerical methods. Then a single flapping wing and three flapping wings in a tandem arrangement are accomplished respectively. It founds that the mean thrust coefficient of three plate wings is bigger than the one of the single plate wing. Three ellipsoidal wings and single ellipsoidal wing are compared. It shows that the single ellipsoidal wing has larger thrust coefficients than the three ellipsoidal wings. Ellipsoidal flapping wing and plate wing were further compared to investigate the influence of wing shape. It indicates the mean thrust coefficient of the ellipsoidal wing is bigger than the plate wing.

Recently, countries at high latitudes have updated their vitamin D recommendations to ensure adequate intake for the musculoskeletal health of their respective populations. In 2010, the dietary guidelines for vitamin D for Canadians and Americans aged 1–70 years increased from 5 μg/d to 15 μg/d, whereas in 2016 for citizens of the UK aged ≥4 years 10 μg/d is recommended. The vitamin D status of Canadian children following the revised dietary guidelines is unknown. Therefore, this study aimed to assess the prevalence and determinants of vitamin D deficiency and sufficiency among Canadian children. For this study, we assumed serum 25-hydroxy vitamin D (25(OH)D) concentrations <30 nmol/l as ‘deficient’ and ≥50nmol/l as ‘sufficient’. Data from children aged 3–18 years (n 2270) who participated in the 2012/2013 Canadian Health Measures Survey were analysed. Of all children, 5·6 % were vitamin D deficient and 71 % were vitamin D sufficient. Children who consumed vitamin D-fortified milk daily (77 %) were more likely to be sufficient than those who consumed it less frequently (OR 2·7; 95 % CI 1·4, 5·0). The 9 % of children who reported taking vitamin D-containing supplements in the previous month had higher 25(OH)D concentrations (OR 6·9 nmol/l; 95 % CI 1·1, 12·7 nmol/l) relative to those who did not. Children who were older, obese, of non-white ethnicity and from low-income households were less likely to be vitamin D sufficient. To improve vitamin D status, consumption of vitamin D-rich foods should be promoted, and fortification of more food items or formal recommendations for vitamin D supplementation should be considered.

The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis.

Long sediment cores (12.5 and 13.5 m) from two lakes in Yunnan Province were used to infer the paleoclimate of southwest China over the past 50,000 yr. During the Holocene and marine isotope stage (MIS 3), bio-induced carbonate precipitation and organic matter (OM) production was high, suggesting warm temperatures and high primary productivity. In contrast, sediment inorganic carbon (IC) and organic carbon (OC) concentrations were low in last glacial deposits from 38,000 to 12,000 cal yr B.P., indicating cool temperatures and low productivity. The 50,000-yr record has alternating peaks of carbonate and coarse-grain (>38 μm) quartz that reflect warm, moist interglacial or interstadial conditions alternating with cold, dry glacial or stadial conditions, respectively. Spectral analysis of the carbonate and quartz signals reveals power concentrated at periods of 7200 and 8900 cal yr, respectively, that may reflect a nonlinear climate response to precessional forcing at a time of reduced eccentricity modulation (McIntyre and Molfino, 1996). Oxygen isotope values of calcite from Yunnan lake cores indicate the summer monsoon was weak during the last glaciation from 50,000 to 12,000 cal yr B.P. The summer monsoon intensified between 12,000 and 8000 cal yr B.P., but weakened gradually in response to insolation forcing during the mid-to-late Holocene. Our results support the Overpeck et al. (1996) model that posits a weak summer monsoon during the last glaciation that responded nonlinearly to insolation forcing when its intensity was affected by Eurasian snow cover and ice-sheet extent. The summer monsoon intensified and responded linearly to seasonal insolation forcing in the Holocene when ice volume diminished.

Foxtail millet (Setaria italica (L.) P. Beauv.) is a naturally stress-tolerant plant, a major reserve crop and a model for panicoid grasses. The recent completion of the S. italica genome facilitates identification and characterization of WRKY transcription factor family proteins that are important regulators of major plant processes, including growth, development and stress response. The present study identified 103 WRKY transcription factor-encoding genes in the S. italica genome. The genes were named SiWRKY1–SiWRKY103 according to their order on the chromosomes. A comprehensive expression analysis of SiWRKY genes among four different tissues was performed using publicly available RNA sequencing data. Eighty-four SiWRKY genes were more highly expressed in root tissue than in other tissues and nine genes were only expressed in roots. Additionally, real-time quantitative polymerase chain reaction was performed to comprehensively analyse the expression of all SiWRKY genes in response to dehydration. Results indicated that most SiWRKY genes (over 0.8) were up-regulated by drought stress. In conclusion, genome-wide identification and expression profiling of SiWRKY genes provided a set of candidates for cloning and functional analyses in plants’ response to drought stress.

A new approach is proposed to analyze Bremsstrahlung X-rays that are emitted from laser-produced plasmas (LPP) and are measured by a stack type spectrometer. This new method is based on a spectral tomographic reconstruction concept with the variational principle for optimization, without referring to the electron energy distribution of a plasma. This approach is applied to the analysis of some experimental data obtained at a few major laser facilities to demonstrate the applicability of the method. Slope temperatures of X-rays from LPP are determined with a two-temperature model, showing different spectral characteristics of X-rays depending on laser properties used in the experiments.